SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching P25356 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MNSIINAASKVLRLQDDVKKATIILGDILILQPINHEVEPDVENLVQHEL    50
  51  TKIIQGYPIQDNMIINSKKGTVEDDLCELNNYTCFALSKSFDLCHDSRNF   100
 101  NIAQPKRWIQLLETLTDSVSFAVIVQIILTLSNISLINKQTLGKLKKLRI   150
 151  RIFEILSNKNDSWKSTLLQKNLIEWYIFMLSVDCTPLELQNLYLHKELKF   200
 201  CNGILNSLTLQVSDPRSQNYLQFENTYKLFQIQKSSRINNSFLFYIEFNS   250
 251  VTSNRIMTIERHIYLEIKEGQFCISNDNYIIGLFENFEFEAGTLYFIGVL   300
 301  IDHNNRITLYVDGSMINQLTLFENSICQLSTCELGSMICSIKVYRFYLWD   350
 351  GLLTEFAINILQAIGTNYQYTFSKKKEGPEVLSLCQDFLIAKAHLMARPT   400
 401  TEISSTKYIDEIELLEMENIIIDVNPNDILQDFTESSNFTVKFEESTNSK   450
 451  NIPEVGKCYFYRSSNLVSKFVSIDSIRLAFLNMTESGSIDDLFHHVSHLM   500
 501  NLLRNIDILNWFKKDFGFPLFAYTLKQKITQDLSQPLNIQFFNLFLEFCG   550
 551  WDFNDISKSIILDTDAYENIVLNLDLWYMNEDQSSLASGGLEIIRFLFFQ   600
 601  ISSLMEASIYSKFNSNKFNDMNILEKLCLSYQAVTKRENQNSKFNELSSD   650
 651  LISVFVTLLKSNTDKRHLQWFLHLSYYFIKRKDVRSTEIILQAVDQLFSF   700
 701  YLDQGSDENAKILSEIIPLKLILMIMDQIVENNESNPITCLNILFKVVLT   750
 751  NKPLFKQFYKNDGLKLILTMLCKVGKSYREEIISLLLTYSIGNYTTANEI   800
 801  FSGAEDMIGGISNDKITAKEIIYLAVNFIEWHVINSNASDSSSVLDLNNH   850
 851  ILRFVEDLKSLSAVPINESVFDPKKSYVMVSLLDLSIALNESEDISKFKS   900
 901  SSKVISELIKGNIMCALTKYAAYDFEVYMSTFFCHSTEYKLVYPKTVMNN   950
 951  SSYLELSFIVTLLPEILNDLVDSNNNLNLMMLKHPYTMSNLLYFLRKFRP  1000
1001  DTSQIVMPKDFYFSSYTCLLHCVIQIDKSSFYHFKNVSKSQLLQDFKICI  1050
1051  MNLIYSNTLKQIIWEKEEYEMFSESLMAHQEVLFAHGACDNETVGLLLIF  1100
1101  FANRLRDCGYNKAVFNCMKVIIKNKERKLKEVACFFDPANKSEVLEGLSN  1150
1151  ILSCNNSETMNLITEQYPFFFNNTQQVRFINIVTNILFKNNNFSPISVRQ  1200
1201  IKNQVYEWKNARSEYVTQNNKKCLILFRKDNTSLDFKIKKSISRYTYNLK  1250
1251  TDREENAVFYRNNLNLLIFHLKHTLEIQSNPNSSCKWSSDFAEDFDGMKR  1300
1301  RLLPAWEPKYEPLINEEDANQDTITGGNRQRRESGSILSYEFIEHMETLE  1350
1351  SEPVGDLNENRKILRLLKDNDSIATIWNCSLIIGLEIKEGILIHGSNYLY  1400
1401  FVSDYYFSLEDKKILKLSEVSQESRDMTVSLINGPDVKRVSTFLKHEVFV  1450
1451  WKLLDITFVTKRPFLLRDVAIELLFKERVSAFFSFYNKRVRDDVLRVLNK  1500
1501  IPKHLPADPIFSSVLQEINDRGNSIVARNGIGKASIASKFTSVFSANNSL  1550
1551  IDGFEISKKWVRGEISNFYYLLSINILAGRSFNDLTQYPVFPWVIADYES  1600
1601  NVLDLENPKTYRDLSKPMGAQSEKRKLQFIERYEALASLENADSAPFHYG  1650
1651  THYSSAMIVSSYLIRLKPFVESFLLLQGGSFGPADRLFSSLERAWSSASS  1700
1701  ENTTDVRELTPEFFFLPEFLINVNSYDFGTDQSGKKVDDVVLPPWANGDP  1750
1751  KVFIQKNREALESPYVSAHLHEWIDLIFGYKQKGDIAVKSVNVFNRLSYP  1800
1801  GAVNLDNIDDENERRAITGIIHNFGQTPLQIFQEPHPEKIACNVQQLTTE  1850
1851  VWRKVPMKPIFEKTIFNLNEKNRSVDYVIHDPSYFDSLYWRGFAFPNLFF  1900
1901  RTEESLVSLRIVHKNWLKIGLDIFKKTHMAQITSFAYWKLGEFITGDKNG  1950
1951  LIKVWKYRKDKHSVSGNLENKKTMFGHLCELKEMRCYHDYNTLLTLDISG  2000
2001  LVYVWDMINFELVRQITNDAQKVAISQHAGSIMVLTKNNAISIFNLNGQI  2050
2051  YTSKKFEPAKIVSSIDFFDFTKLDAGYRKHIYWKEMEILLVGFEDGTIEI  2100
2101  YELFLNFHNEWAIKLLKQLCTEKGKAITSIKGQGKTYLSQKRRKDTAEPH  2150
2151  EIEVIAGTLDGRLAIWY                                   2167

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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